'Free Libya fighting groups have been developed from the bottom up and independently of one another.' Photograph: Carl De Souza/AFP/Getty

On Monday in Misrata more than 500 Libyans held their first demonstration against the new interim government. The protest materialised after the National Transitional Council lined up Albarrani Shkal, a former Gaddafi general, as head of security in the capital, Tripoli.

On the one hand, Shkal's appointment can be considered a positive and necessary move: integrating former regime loyalists will be integral to the building of a stable Libya, lest these loyalists become disenfranchised and seek to undermine stability as a means of remedying their marginalisation.

However, it will be difficult to apply such arguments in the case of top-tier loyalists who either refused to switch sides, switched sides too late or who have the blood of too many innocent civilians on their hands.

Many Libyans will feel that these objections apply to Shkal, who only defected to the opposition in May and had been operations officer for the brutal and infamous 32nd brigade led by Gaddafi's son Khamis responsible for the death of hundreds, perhaps thousands, of innocent civilians.

But the protests should not be taken at face value. The challenge of securing Tripoli and the broader country is made difficult by the divided interests, ambitions and loyalties within the anti-Gaddafi forces.

Although there has to be continuity in the security establishment – that is, retaining former regime military personnel and law enforcement officers – the process of doing so will depend on whether the NTC can actually organise the thousands of fighters that it calls the "official" NTC army but which actually constitutes an array of disparate military units.

"Free Libya" fighting groups have been developed from the bottom up and independently of one another, with the two primary fighting forces coming from the east (the original and official NTC army) and the west, which over the past few weeks made the most decisive contribution to the conflict by tightening the noose around Tripoli.

There has been some co-ordination between the two groups but a unified command structure integrating them both does not exist.

What will compound this organisational gap is the series of figures contesting for the top job of military chief. Before his suspicious death, former regime interior minister Abdul Fatah Younes was the opposition army commander in Benghazi. However, he was challenged for this position by the experienced, and influential, Khalifa Hifter, as well as Omar al-Hariri (both Benghazi based).

But groups in the west also have their own battle-hardened leaders, including Anwar Fekini, a former lawyer who has led the resistance from the west, where the rebellion was fiercest and also comprised of the Berber minority that has long been neglected and repressed by the regime but who now make up some of the most effective fighting units.

So far, brigades in both Misrata (located in the east) and the Nafusa mountains (the west) have refused to either recognise the authority of the NTC or reject the notion that they unreservedly take orders from NTC leaders. On Monday, for example, Misrata's ruling council warned that if Shkal's appointment was confirmed then its military units would refuse to follow NTC orders.

Similarly, little has been said about the Islamist groups who could also end up undermining post-Gaddafi Libya.

This is not necessarily because the Islamists may end up being serious contenders in the political arena but because they have some of the most effective, organised and heavily armed military brigades that have acted independently of the NTC.

As well as having the death of Younes attributed to them, the Islamists gained further recognition of their strength in the recently released draft constitution, which regards Islamic jurisprudence (sharia) as "the principal source of legislation" – clearly a measure of appeasement.

Balancing these divided interests will further depend on whether the NTC is able to reconcile its own political differences, given that it comprises an array of individuals with conflicting political and ideological ambitions. There is also the question of whether they can organise themselves quickly enough to manage the overwhelming logistical and organisational demands that come with the paying of salaries and the immediate provision of basic services and humanitarian assistance – for the entire country.

There is still reason to be more than just cautiously optimistic, though. Libya is no Iraq. There is little room for any sectarian or ethnic violence to erupt and no ethnic or sectarian transfer of power. People will grind their axes, that is inevitable, and politics may turn violent, but the worst can be avoided if competing interests and ambitions are balanced – which is possible, since there is enough to go around for everyone.